DeBoer became an assistant coach for the Detroit Junior Red Wings during the 1994-95 season. During the 1995 off-season, the club was renamed the Detroit Whalers, and DeBoer was promoted to the dual position of head coach-general manager as Paul Maurice left the team to become the coach of the Hartford Whalers in the NHL. DeBoer guided the Whalers to a first place finish in the West Division, as Detroit advanced to the third round in the playoffs. In 1996-97, Detroit struggled to a 26-34-6 record and was eliminated in the first round of the post-season.

The Whalers renamed themselves to the Plymouth Whalers during the 1997 off-season, and the team rebounded to a second place finish in the West Division with a 37-22-7 record, and for the second time in three seasons they advanced to the third round of the playoffs. In 1998-99, DeBoer led the team to a league leading 106 points, earning them the Hamilton Spectator Trophy, and DeBoer winning the Matt Leyden Trophy as OHL Coach of the Year. Plymouth had a disappointing playoff run though, as they were defeated by the underdog London Knights in the second round of the playoffs.

In 1999–2000, Plymouth once again had the best record in the league, earning DeBoer his second straight Matt Leyden Trophy. The Whalers advanced all the way to the J. Ross Robertson Cup finals, before losing to the Barrie Colts 4-2 in the seventh and deciding game.

The Whalers had another very successful season in 2000-01, winning the West Division for the third consecutive season, and having the second best record in the league. Plymouth got hot in the playoffs, winning their first nine games, and advanced to the J. Ross Robertson Cup for the second season in a row. In the final round, Plymouth lost to the Ottawa 67's in six games.

After the season, both DeBoer and his assistant, Steve Spott, decided to leave the Whalers and join the Kitchener Rangers in similar positions.

DeBoer took over a Kitchener team that had missed the playoffs in the previous season and finished 10 games under .500, and quickly the club showed improvement, as the Rangers finished in third place in the Midwest Division with a 35-22-10-1 record. The team was then swept in the first round of the playoffs by their Highway 7 rivals, the Guelph Storm.

The Rangers continued to improve in the 2002-03 season, winning the Hamilton Spectator Trophy as Kitchener had a league best 100 points. In the playoffs, the Rangers quickly swept the Sault Ste. Marie Greyhounds in the first round, followed by a five game series win over the Guelph Storm, setting up a Western Conference matchup against DeBoer's former team, the Plymouth Whalers. After the Whalers won the fifth game by a 2-1 score in overtime to take a 3-2 series lead, the Rangers rebounded and staved off elimination by winning the final two games of the series, advancing to the J. Ross Robertson Cup finals against the Ottawa 67's. Ottawa took the series opener, however, Kitchener rebounded and won four in a row to win the cup and earn a berth in the 2003 Memorial Cup. DeBoer led the Rangers to a perfect 3-0 record during the round-robin portion of the tournament, sending Kitchener to the finals against the Hull Olympiques. The Rangers would easily defeat Hull 6-3 in the game to win their first Memorial Cup since 1982.

Kitchener saw themselves in a rebuilding season in 2003-04, however, DeBoer helped the club finish fourth in the Western Conference with a 34-26-6-2 record, but the team struggled in the playoffs, and lost to the Plymouth Whalers in five games in the opening round. The 2004-05 season saw the team once again finish in third in their division and fourth in the conference. DeBoer led the Rangers to a first round victory over the Erie Otters, then helped Kitchener to a stunning series sweep over the powerful Owen Sound Attack. In the third round, the Rangers faced the record-setting London Knights, and were quickly eliminated in five games.

In 2005-06, Kitchener saw their point total improve to 96, the third highest in the league, however, they were upset by the Owen Sound Attack in the first round of the playoffs. The team increased their point total to 98 in the 2006-07 season, finishing third in the Western Conference, and easily sweeping the Sarnia Sting in the first round. Kitchener would struggle in the second round, losing in five games to the Plymouth Whalers.

With the Rangers being named the host of the 2008 Memorial Cup, Kitchener put together one of the best regular season's in OHL history, finishing with a 53-11-4 record, earning a league high 110 points to win the Hamilton Spectator Trophy. The DeBoer led Rangers quickly swept the Plymouth Whalers and Sarnia Sting in the first two rounds, before disposing the Sault Ste. Marie Greyhounds in the Western Conference finals. In the J. Ross Robertson Cup finals, the Rangers took the first three games of the series, however, the Belleville Bulls rebounded and took the next three games, setting up a seventh game at the Kitchener Memorial Auditorium. In the last game of the series, the Rangers defeated the Bulls 4-1 to win the championship. During the 2008 Memorial Cup, the Rangers had a 2-1 record in the round-robin, setting up a rematch against the Bulls in the semi-finals. Kitchener exploded for a 9-0 win, and would face the Spokane Chiefs in the final game. The Chiefs spoiled the Rangers party though, defeating Kitchener 4-1.

DeBoer decided to take the next step in his career, and on June 13, 2008, he was named head coach of the Florida Panthers in the National Hockey League. DeBoer led the Panthers who then finished with the second best point total in team history, as they had a 41-30-11 record, earning 93 points, just behind the 1999–2000 Panthers, who had 98. The 93 points though was not enough for the Panthers to earn a post-season berth, as they finished in ninth in the Eastern Conference.

In the 2009-10 season, the Panthers struggled, as they finished with a 32-37-13 record, earning 77 points, and last place in the Southeast Division. The 77 points was the lowest point total by the Panthers since 2003-04. The Panthers continued to struggle in the 2010-11 season, as Florida finished in last place in the Eastern Conference with a 30-40-12 record, earning 72 points. After the season, the Panthers fired DeBoer with one year remaining on his contract.[1]

He was hired on July 19, 2011 by the New Jersey Devils following two interviews with Devils GM Lou Lamoriello.[2] In his first season, DeBoer posted career highs in wins and point totals, guiding his team to the Stanley Cup playoffs for the first time in his coaching career. The Devils beat their first round opponent, DeBoer's former team the Florida Panthers, in double overtime in game seven. The Devils would also go on to dispatch the Philadelphia Flyers in five games in round two and the New York Rangers in six games in the Eastern Conference Finals. It was the first time the New Jersey Devils had reached the Stanley Cup Finals since 2003. The Devils lost the 2012 Stanley Cup Finals to the Los Angeles Kings in six games.

The Devils slipped into last place in the Atlantic Division in the 2012-13 season, going 19-19-10, earning 48 points, and failed to qualify for the playoffs.

In 2013-14, the Devils began the year with a 1-5-3 record, and were not able to rebound from their poor start, finishing sixth in the new Metropolitan Division with a 35-29-18 record, failing to qualify for the post-season for their second straight season.